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Thread: Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula

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    Quote Originally Posted by artemv View Post
    We have 2 possibly Epigravettian Y-happlogroups in the Middle East:
    - R1b-V88
    - I2-Y16649
    Both are minor happlogroups, and indeed were not found in any ancient human remains in Middle East.
    But their TRMCA gives us information that they likely arrived to the Middle East very early, before 12k ybp.
    I agree that Villabruna-type ancestry arrived in the Middle East very early. But I'm not sure the V88 in modern Near East/Africa can be linked directly to Epigravettian-era expansions (and I think this type of ancestry is pre-Epigravettian anyway). Even though basal V88 is supposed to be ~18,000 years old, the TMRCA is only <12kya, and nearly all modern V88 guys belong to clades even younger than that. If you look for example at the R-Y7777 subclade it only formed 9500 BP and has members in places as diverse as Britain, Italy, Egypt and Benin. This is probably a "Villabruna" haplogroup, but it only really expanded across MENA long after the Epigravettian-- most likely w/Cardial Neolithic farmers or something. But Iberomaurusians had plenty of Villabruna-related ancestry as early as 15kya, so the Cardial Ware cannot be the earliest wave of this type of ancestry into MENA.

    One theory: "Common West Eurasian" (see qpgraoh below) split into 2 groups upon arriving in southeastern Europe: one group immediately spread into Anatolia, the Levant and North Africa prior to the LGM (Levantine Aurignacian?), while the other group "stayed home", only spreading into western Europe and replacing Magdalenians/Gravettians beginning around 20kya. I would expect the carriers of this type of "proto-Villabrunan" ancestry to belong to basal clades of G, I, or J to be honest. This could also explain how those basal clades of J* ended up in Socotra...

    Consider the huge drift magnitudes from Common West Eurasian to Villabruna, and to Dzudzuana's non-Basal ancestry in the gpGraph from the Dzudzuana paper (circled in red): this would be consistent with "deep" geographic separation between two populations descended from Common West Eurasian: consistent with one branch migrating to MENA pre-LGM, and the other spending much of the LGM in southern/southeast Europe.

    Last edited by K33; 03-16-2019 at 03:09 AM.

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    Generallisimo has generously been running some qpgraphs for me: I've been trying to create one that includes every major Neolithic and earlier population. So far this is the result.

    The worst outlier is Z 3.987, with Iron_Gates_HG being overfit to Kostenki14, but this is a small issue that will likely only require minor adjustment (maybe a bit of GoyetQ116-1 into Iron_Gates_HG)
    It replicates some of the features seen above, such as Vestonice being a mix of Sunghir and something WHG-like, ANE being an East-West mix.
    The key difference between this graph and others (like the above) is that there is no Basal Eurasian. It's not needed as long as East Eurasians receive an input from a Goyet-related branch.
    Note that AG3 was initially in the graph, and fit unadmixed off the ANE node, but it had to be dropped to save the snp count.
    Last edited by Kale; 03-16-2019 at 04:12 AM.
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    Quote Originally Posted by Kale View Post
    Generallisimo has generously been running some qpgraphs for me: I've been trying to create one that includes every major Neolithic and earlier population. So far this is the result.

    The worst outlier is Z 3.987, with Iron_Gates_HG being overfit to Kostenki14, but this is a small issue that will likely only require minor adjustment (maybe a bit of GoyetQ116-1 into Iron_Gates_HG)
    It replicates some of the features seen above, such as Vestonice being a mix of Sunghir and something WHG-like, ANE being an East-West mix.
    The key difference between this graph and others (like the above) is that there is no Basal Eurasian. It's not needed as long as East Eurasians receive an input from a Goyet-related branch.
    Note that AG3 was initially in the graph, and fit unadmixed off the ANE node, but it had to be dropped to save the snp count.
    Interesting, but isn't "NodeA" basically Basal Eurasian? It splits off from the trunk after Mbuti but before the East and West Eurasians, and contributes the majority of Iberomaurusian's ancestry... also Natufian and Anatolia_N are pretty important blank spots; if they are added and demand admixture from NodeA that's basically confirmation it's a stand-in for Basal Eurasian, right?

    That's one of the reasons I trust the Dzudzuana gpGraph the most for now, at least until the Dzudzuana raw data is made public. Dzudzuana is such a critical anchor point both in time and space.

    I think a big reason Basal Eurasian seems nebulous sometimes is that it's split time, IMO, is much earlier than some of the initial estimates (it's closer to 100kya than 60kya). This is one of the reasons why Anatolia_N was estimated as 44% Basal, then revised down to 14% Basal in one follow-up paper, then finally pegged at 28% in the Dzudzuana paper for example. It's difficult to model such an old and deep splinter group, with no samples earlier than the Mesolithic...

    That's interesting WHG is modeled as Gravettian + ~20% ANE admix. That would explain the R1b spread thinly throughout the Villabruna Cluster samples.

    Also "NE1" would match the Ancient Central Eurasian population I've speculated about. This ghost seems to keep popping up in one form or another whenever CHG or Iran_N go into qpGraph...
    Last edited by K33; 03-16-2019 at 06:07 AM.

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    Quote Originally Posted by K33 View Post
    The eruption wiping out humans in South Europe/Balkans is still up for debate, Oase is just a single sample. But just to be clear, are you saying the Phlegraean Eruption annihilated Basal Eurasians in the Levant too?
    Not sure. Maybe.

    Quote Originally Posted by K33 View Post
    I don't see any mention of the Kunda/Narva samples in the Dzudzuana paper...
    See figure 6a (and b) of that paper.

    Quote Originally Posted by K33 View Post
    Also, the Gravettians/Vestonice only contributed ~10% of their ancestry to Villabruna per Fu et al; thus Epigravettian/Villabruna was not a continuation of the Gravettian/Vestonice culture but an intrusive disruption of it...
    The same paper suggest that it is unlikely that Villabruna is the only type of ancestry to survive the LGM unaffected and states that it can be modeled as a mixture of Vestonice, Dzudzuana and a tad AG3. Considering that the Epigravettian was called that way for a good reason I think that is pretty much the way it went.

    Quote Originally Posted by K33 View Post
    ? Is that why all non-Baltic modern Europeans have substantially more Neolithic autosomal ancestry than WHG ancestry? (excluding the WHG-related ancestry brought via Corded Ware/Yamnaya pastoralists)?
    The onset of Y-DNA I was male biased. See Mathieson 2018.
    Last edited by epoch; 03-16-2019 at 12:06 PM.

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    Quote Originally Posted by K33 View Post
    Interesting, but isn't "NodeA" basically Basal Eurasian? It splits off from the trunk after Mbuti but before the East and West Eurasians, and contributes the majority of Iberomaurusian's ancestry
    But Ganj_Dareh_N (Iran_N) derives 0% from NodeA in that graph. Even if you wanted to call NodeA basal, Iran_N still need no basal there.
    ... also Natufian and Anatolia_N are pretty important blank spots; if they are added and demand admixture from NodeA that's basically confirmation it's a stand-in for Basal Eurasian, right?
    Barcin_N is the next pop I'm trying to fit in, but the graph as it stands is very complex though and that one small addition seems to be the straw breaking the camel's back, and qpgraph is having issue completing it, it's getting stuck and not able to finish.
    I gave Barcin_N an admixture from pre-Taforalt in the hopefully forthcoming graph though because I fully suspect Barcin_N to require ~12% Taforalt-like ancestry. This doesn't make NodeA basal Eurasian because, as mentioned, Iran_N is a population with supposed basal and doesn't need any NodeA.
    Last edited by Kale; 03-16-2019 at 03:30 PM.
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    Quote Originally Posted by Kale View Post
    But Ganj_Dareh_N (Iran_N) derives 0% from NodeA in that graph. Even if you wanted to call NodeA basal, Iran_N still need no basal there.
    True, but Ganj_Dareh DOES take 52% ancestry from "West1", which is a mere 55 drift units away from NodeA. 52% of Gan_Dareh's ancestry traces directly to a source only 198 drift units (143+40+15) from NodeA. And 66% of Ganj_Dareh is derived from sources only 297 drift units from "Eurasia" (if you include the "East0" anchor directly contributing to NE1).

    Look at the other historical anchors:
    GoyetQ116, Vestonice16, Kostenki14, Tianyuan all get 100% of their ancestry from "Eurasia" too-- but they all require 450+ drift units from "Eurasia" to account for their position. And these guys are all 30kya-45kya old-- much, much, older than Ganj_Dareh. If Basal Eurasian wasn't real, all other things equal these guys should be less drifted from "Eurasia", but the opposite outcome shows ipso facto Ganj_Dareh is phylogentically closer to the basal OOA groups...

    Basically NodeA could be renamed "Ancestral North African" and "Eurasian" could be renamed "Basal Eurasian", and it's not all too different from the Dzudzuana graph.

    Interestingly the most "basal" of the Crown Eurasians in the gpGraph are Sunghir and Ust Ishim-- but perhaps it's telling they were both genetic dead-ends.

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    Quote Originally Posted by K33 View Post
    True, but Ganj_Dareh DOES take 52% ancestry from "West1", which is a mere 55 drift units away from NodeA.
    A true 'basal Eurasian' should be equally related to all 'crown Eurasians', but less related to crown Eurasians than crown Eurasians are to each other. West1 does not match that criteria. It shares 40 units of drift with archetypal West Eurasian populations.
    If West1 were to be sampled in pure form, it would be more related to say Kostenki14 than it would be to Tianyuan.

    Look at the other historical anchors:
    GoyetQ116, Vestonice16, Kostenki14, Tianyuan all get 100% of their ancestry from "Eurasia" too-- but they all require 450+ drift units from "Eurasia" to account for their position.
    An important technical detail of qpgraph is that any drift edge leading to a single sample is not informative. Compare those to the drift edge to Sunghir (multiple samples combined), the drift is only 42.
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    Quote Originally Posted by K33 View Post
    I think a big reason Basal Eurasian seems nebulous sometimes is that it's split time, IMO, is much earlier than some of the initial estimates (it's closer to 100kya than 60kya). This is one of the reasons why Anatolia_N was estimated as 44% Basal, then revised down to 14% Basal in one follow-up paper, then finally pegged at 28% in the Dzudzuana paper for example. It's difficult to model such an old and deep splinter group, with no samples earlier than the Mesolithic...
    That is a really interesting idea, considering that more and more evidence surfaces of AMH in West-Asia before 100 K years ago.

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    Quote Originally Posted by epoch View Post
    That is a really interesting idea, considering that more and more evidence surfaces of AMH in West-Asia before 100 K years ago.
    I personally believe the phylogeny goes something like this:

    350kya-200kya: Various "Basal African" lineages split from the trunk in Sub-Saharan Africa (Central and West isolated in rainforests for example)
    150kya-100kya: "Basal Eurasian"-related lineages split from the trunk, with nodes forming in the Maghgreb, Nile Valley, and Arabia and sporadic gene flow between them
    70kya-60kya: Crown Eurasians split off from the Arabian population, possibly by crossing over the Zagros range

    Quote Originally Posted by Kale
    An important technical detail of qpgraph is that any drift edge leading to a single sample is not informative. Compare those to the drift edge to Sunghir (multiple samples combined), the drift is only 42.
    Ahh, I did not realize that. Interesting.

    However, the fact that Barcin makes the tree fall apart is IMO telling... I think you will need a Basal node in there to properly model Anatolia_N and Dzudzuana.

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    Quote Originally Posted by Kale View Post
    Generallisimo has generously been running some qpgraphs for me: I've been trying to create one that includes every major Neolithic and earlier population. So far this is the result.

    The worst outlier is Z 3.987, with Iron_Gates_HG being overfit to Kostenki14, but this is a small issue that will likely only require minor adjustment (maybe a bit of GoyetQ116-1 into Iron_Gates_HG)
    It replicates some of the features seen above, such as Vestonice being a mix of Sunghir and something WHG-like, ANE being an East-West mix.
    The key difference between this graph and others (like the above) is that there is no Basal Eurasian. It's not needed as long as East Eurasians receive an input from a Goyet-related branch.
    Note that AG3 was initially in the graph, and fit unadmixed off the ANE node, but it had to be dropped to save the snp count.
    In a separate thread recently, I mentioned how I suspect there isn't really a neat cleavage between West and East Eurasians, basically I think very early on in the Eurasian expansion there was some bi-directional gene flow between proto-West and proto-East populations. In the case of West Eurasians, I guess we don't need to go that far back to find confirmation of admixture, since we know ANE had some East-Eurasian stuff in it, and pretty much all West Eurasians today have some level of ANE. Right now we don't have solid evidence yet of early West > East flow, however the excess affinity Goyet shares to Tianyuan might be a possible hint of something like that?

    The reason I mention this, is because in this graph's topology, there is no such thing as pure, living unadmixed West or East Eurasian, as the graph has West5 mixing into ancestral East1. It's nice to see some confirmation of my intuition, however I realize this is just a single graph and we don't have much in the way of Upper Paleolithic East Eurasian DNA yet. The one thing I noticed, there isn't really a representative of an ostensibly "pure" East Eurasian population other than Tianyuan, the East Eurasian sources are all branches modeling different ANE populations. Do you think if you throw in a population like Han or Ami (or hell, even Onge or Papuan), you could still get an early branch of something West mixing into ancestral East sources?

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